Workshops

Prerequisites

These workshops are hands-on whenever possible. Since they are hands-on, they have prerequisites. If you don't meet the prerequisites, then you won't get much out of the workshop. If you don't have the prerequisites for most of the workshops, then you won't get much out of the day. Our goal is that when you walk out of a workshop, you will have some actual experience with the workshop topic. Please read the prerequisites for workshops before deciding if you should attend.

Prerequisites for all workshops

A wifi enabled laptop, or a buddy with such a laptop who will let you sit and work with them.

While you can use any running Galaxy instance, we strongly recommend that you use the conference provided virtual machine image, and that you have it installed and running before arriving at the conference.

WS3

Want the power of Galaxy without the compute infrastructure overhead? Need to run compute-intensive analysis, but only from time to time? Learn how to set up your own elastic, and fully populated (tools and reference data) Galaxy instance using Amazon Web Services.

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.

Results

You will have created a Galaxy server on Amazon Web Services using CloudMan. You will access to this server if you wish to use it during subsequent workshops.

WS4

This workshop will introduce participants to the high-level architecture of Galaxy internals, and to the project's coding practices and standards. Then, rather than try to cover all areas at a shallow depth, we will specifically focus on the implementations of workflows and the API. The workshop will finish with participants extending the API in their Galaxy instance.

You will have a high-level understanding of Galaxy's software architecture, a specific knowledge of how workflows and the API are implemented, and will have added an additional API call to your Galaxy instance.

You will have access to personal Galaxy server that you can use in subsequent workshops during the day. This may be Galaxy installed directly on your Linux laptop, Galaxy installed on a virtual machine on your PC or Mac, or access to an Amazon Web Services EC2 instance with Galaxy installed on it.

WS7

The Galaxy tool shed is a place for the Galaxy community to share functionally correct Galaxy tools, proprietary Galaxy data types and exported Galaxy workflows. Tools in the tool shed should have been built within a proprietary development environment that included a local Galaxy instance in which they were proven to be functionally correct before they were uploaded to the tool shed. Demonstrating the use of the tool shed excludes discussions about developing the tools, proprietary datatypes or workflows that are stored there.

WS8

Participants in this workshop will use simulation to develop familiarity with the performance of basic SNP and indel detection methods.

By comparing variant detection results under different conditions to the known set of true variants produced by the simulation, participants will assess the effects of standard practices such as base quality recalibration, indel realignment, and variant quality filters.

This hands-on workshop will demonstrate basic RNA-Seq transcript level comparison analysis using the Tophat (Bowtie), Cufflinks, Cuffmerge and Cuffdiff tools in Galaxy. We will compare the expression of genes under two conditions.

We will demonstrate this analysis both with an installed reference genome and with a non-installed organism.

Sample datasets small enough to be successfully processed during the course of the seminar will be provided. Participants will perform the analyses themselves on the provided cloud instance of Galaxy.

Torrent Suite Software is an open source platform that automates the analysis of data streaming from the Ion Torrent Personal Genome Machine and Proton Sequencers. Torrent Suite provides an intuitive web interface and a flexible Software Development Kit (SDK) that enables users to develop plugins which quickly and easily expand the analysis capabilities of Torrent Suite Software. The SDK includes a powerful API that for interacting directly with the system. In this workshop, attendees will learn more about Torrent Suite Software and how to leverage the SDK to write plugins and work with the API, including how to push data into Galaxy. We will also cover Ion Torrent's developer community support programs.

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.